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Like the checking for messages notification on Android, I use notification reminder app to remind me of missed messages (ring every 5 minutes) and sometimes randomly in the middle of the night Signal creates a notification that says "checking for messages" and it stays there for a while getting my notification remjnder to think there is an unread message and ringing in the middle of the night. I can't turn off notifications I might need to be waken up for important stuff.
You could use Tasker to make an automation that checks what the notification's content is, but it's just an ugly workaround
I think it might have a good reason to post that notification. Android kills apps that are doing background operations for too long without also posting a persistent notification about it.
You can disable the notification channel corresponding to that kind of notification, though. I'm not totally sure if that way your other app won't see it either, but I think it's worth a try.